SMTL ID : 5a7s.2 (1 other biounit)

Crystal structure of human JMJD2A in complex with compound 44

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: S2X.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.5

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.256, H.262, C.328, S.329, C.330 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.256, A:H.262, A:C.328, A:C.330

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain A: G.192, Y.197, Y.199, E.212, S.310, T.311, N.312 Ligands: S2X.11 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.212, A:S.310, A:N.312 Water bridges: A:Y.199, A:Y.199, A:D.213, A:S.218 EDO.4: 7 residues within 4Å: Chain A: E.242, K.246, E.257, A.258, F.259, L.260, Y.297 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.259, A:L.260 Water bridges: A:E.242, A:E.242 EDO.5: 6 residues within 4Å: Chain A: K.336, S.338, M.339, D.340, W.354, K.355 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.337, A:M.339, A:D.340, A:D.340, A:K.355 EDO.6: 3 residues within 4Å: Chain A: G.99, T.148, F.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.99, A:T.148 EDO.7: 8 residues within 4Å: Chain A: I.172, G.173, R.174, L.175, N.194, T.311, N.312, F.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.173, A:L.175, A:N.312 Water bridges: A:R.176 EDO.8: 5 residues within 4Å: Chain A: E.140, R.141, W.144, P.269, L.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.140 Water bridges: A:L.270 EDO.9: 5 residues within 4Å: Chain A: E.236, I.363, D.364, H.365, T.366 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.363, A:H.365 EDO.10: 3 residues within 4Å: Chain A: A.91, I.93, D.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.91, A:D.157

1 x S2X: 2-(5-acetamido-2-oxidanyl-phenyl)pyridine-4-carboxylic acid(Non-covalent)

S2X.11: 12 residues within 4Å: Chain A: Y.154, Y.199, F.207, H.210, E.212, N.220, K.228, W.230, K.263, H.298 Ligands: MN.1, EDO.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.207, A:W.230, A:K.263, A:K.263 Hydrogen bonds: A:Y.154, A:N.220 Water bridges: A:Y.199, A:S.310 Salt bridges: A:K.228 pi-Stacking: A:F.207 pi-Cation interactions: A:H.210

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.12: 4 residues within 4Å: Chain A: F.249, P.250, G.251, S.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.251, A:S.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korczynska, M. et al., Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors. J.Med.Chem. (2016)

Release Date

2016-01-13

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

LYSINE-SPECIFIC DEMETHYLASE 4A

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